028000
kinetic law: 724133
reactant: 724121
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E1Wdeg
type: Reaction

028066
constant: true
value: 0.21251
name: d2
type: Parameter

724327
stoichiometry: 1.0
species: 027953
type: SpeciesReference

metaid_0000087
unit: 723699
name: hours
type: SBMLUnitsDef

028052
constant: true
value: 0.13056
name: b5
type: Parameter

027974
name: WC-1*
initial amount: NaN
is: SBO:0000252
boundary condition: false
initial concentration: 0.0
type: Species
has only substance units: false
is version of: Q01371
constant: false
in compartment: 023948

028092
constant: true
value: 1.34979
name: m
type: Parameter

028014
kinetic law: 724351
modifier: 724339
product: 724327
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: E1Fptrl
type: Reaction

028082
constant: true
value: 2.8E-4
name: gam2
type: Parameter

028008
kinetic law: 724255
reactant: 724243
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: PWdeg
type: Reaction

723939
stoichiometry: 1.0
species: 027957
type: SpeciesReference

metaid_0000088
unit: 723711
name: arbitrary_units
type: SBMLUnitsDef

028070
constant: true
value: 3.36641
name: d4
type: Parameter

028084
constant: true
value: 2.71574
name: r1
type: Parameter

027986
kinetic law: 723903
product: 723891
reactant: 723879
is version of: GO:0016485
is: SBO:0000181
fast: false
reversible: false
name: E2Ftrl
type: Reaction

028094
constant: true
value: 2.18234
name: k
type: Parameter

028048
constant: true
value: 0.08039
name: b3
type: Parameter

027955
is version of: Q01371
constant: false
type: Species
is: SBO:0000252
boundary condition: false
initial concentration: 5.84748
name: WC-1_1
initial amount: NaN
in compartment: 027948
has only substance units: false

723891
stoichiometry: 1.0
species: 027957
type: SpeciesReference

724459
stoichiometry: 1.0
species: 027969
type: SpeciesReference

028032
constant: true
value: 0.2834
name: a3
type: Parameter

724399
stoichiometry: 1.0
species: 027959
type: SpeciesReference

028034
constant: true
value: 0.46227
name: a4
type: Parameter

028079
constant: true
value: 0.34603
name: gam1
type: Parameter

027992
kinetic law: 723987
reactant: 723975
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: PFdeg
type: Reaction

028109
constant: true
value: 12.0
name: dawn
type: Parameter

028027
constant: true
value: 24.9736
name: a1
type: Parameter

027965
is version of: CHEBI:33699
type: Species
is: SBO:0000250
has only substance units: false
constant: false
is version of: C00046
initial amount: NaN
name: WC-1 mRNA
boundary condition: false
encodes: Q01371
in compartment: 023948
initial concentration: 1.2689

028112
constant: true
value: 24.0
name: dusk
type: Parameter

028045
constant: true
value: 2.13476
name: b2
type: Parameter

028068
constant: true
value: 0.50309
name: d3
type: Parameter

023948
is: GO:0005634
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

723975
stoichiometry: 1.0
species: 027967
type: SpeciesReference

724267
stoichiometry: 1.0
species: 027971
type: SpeciesReference

724206
stoichiometry: 1.0
species: 027961
type: SpeciesReference

028089
constant: true
value: 1.02419
name: n
type: Parameter

028106
constant: true
value: 0.0
name: amp
type: Parameter

027959
is version of: P19970
initial amount: NaN
type: Species
constant: false
boundary condition: false
is: SBO:0000252
initial concentration: 0.09872
has only substance units: false
in compartment: 027948
name: l-Frq_2

028050
constant: true
value: 0.45859
name: b4
type: Parameter

028006
kinetic law: 724231
product: 724219
reactant: 724206
is version of: GO:0006606
is: SBO:0000185
fast: false
reversible: false
name: PWtrl
type: Reaction

027981
kinetic law: 723843
modifier: 723831
product: 723819
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: E1Ftrl
type: Reaction

028016
kinetic law: 724375
reactant: 724363
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E1Fpdeg
type: Reaction

028020
kinetic law: 724435
reactant: 724423
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E2Fpdeg
type: Reaction

027998
is: SBO:0000184
type: Reaction
reversible: false
kinetic law: 724109
name: E1Wtrl
is version of: GO:0006412
modifier: 724097
modifier: 724072
fast: false
modifier: 724084
product: 724060

724483
stoichiometry: 1.0
species: 027969
type: SpeciesReference

028036
constant: true
value: 0.02917
name: a5
type: Parameter

724387
stoichiometry: 1.0
species: 027953
type: SpeciesReference

028077
constant: true
value: 0.14979
name: f2
type: Parameter

028096
constant: true
value: 0.34578
name: a3p
type: Parameter

028030
constant: true
value: 3.59797
name: a2
type: Parameter

027988
kinetic law: 723927
reactant: 723915
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E2Fdeg
type: Reaction

027977
modifier: 723771
modifier: 723747
modifier: 723759
fast: false
name: MFtrn
reversible: false
modifier: 723735
kinetic law: 723783
is: SBO:0000183
product: 723723
type: Reaction
is version of: GO:0006351

724121
stoichiometry: 1.0
species: 027955
type: SpeciesReference

723879
stoichiometry: 1.0
species: 027951
type: SpeciesReference

027957
initial concentration: 0.10647
constant: false
name: s-Frq_2
has only substance units: false
is version of: P19970
type: Species
initial amount: NaN
is: SBO:0000252
boundary condition: false
in compartment: 027948

027990
kinetic law: 723963
product: 723951
reactant: 723939
is version of: GO:0006606
is: SBO:0000185
fast: false
reversible: false
name: PFtrl
type: Reaction

027963
is version of: CHEBI:33699
has only substance units: false
type: Species
name: Frq mRNA
is version of: C00046
is: SBO:0000250
boundary condition: false
in compartment: 023948
constant: false
initial amount: NaN
initial concentration: 0.6935
encodes: P19970

724146
stoichiometry: 1.0
species: 027955
type: SpeciesReference

723711
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

723699
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

028004
kinetic law: 724194
reactant: 724182
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E2Wdeg
type: Reaction

028018
kinetic law: 724411
product: 724399
reactant: 724387
is version of: GO:0016485
is: SBO:0000181
fast: false
reversible: false
name: E2Fptrl
type: Reaction

metaid_0000081
constant: false
name: tot Frq
initial amount: NaN
boundary condition: false
type: Species
is: SBO:0000252
initial concentration: NaN
is version of: P19970
has only substance units: false
in compartment: 023948

724279
stoichiometry: 1.0
species: 027974
type: SpeciesReference

724423
stoichiometry: 1.0
species: 027959
type: SpeciesReference

723819
stoichiometry: 1.0
species: 027951
type: SpeciesReference

723915
stoichiometry: 1.0
species: 027957
type: SpeciesReference

028024
kinetic law: 724495
reactant: 724483
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: PFpdeg
type: Reaction

724363
stoichiometry: 1.0
species: 027953
type: SpeciesReference

027983
kinetic law: 723867
reactant: 723855
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: E1Fdeg
type: Reaction

724303
stoichiometry: 1.0
species: 027974
type: SpeciesReference

028104
constant: true
value: 0.40119
name: gam1p
type: Parameter

028010
fast: false
is version of: GO:0016037
type: Reaction
reversible: true
kinetic law: 724291
is: SBO:0000181
name: PWtrs
is version of: GO:0051091
product: 724279
reactant: 724267

028057
constant: true
value: 0.11167
name: b8
type: Parameter

BIOMD0000000214
rule: metaid_0000086
reaction: 027983
type: SBMLModel
reaction: 027996
parameter: 028050
rule: metaid_0000084
reaction: 028002
parameter: 028084
parameter: 028361
species: 027965
parameter: 028030
species: 027974
parameter: 028045
parameter: 028048
reaction: 027986
units def: metaid_0000088
reaction: 028010
curated: true
reaction: 027977
species: 027971
reaction: 028008
volume units: metaid_0000069
parameter: 028104
parameter: 028061
parameter: 028064
rule: metaid_0000083
parameter: 028077
parameter: 028043
reaction: 028016
reaction: 028020
occurs in: http://identifiers.org/taxonomy/5141
is: MODEL8306015773
name: Akman2008_Circadian_Clock_Model2
is version of: GO:0007623
rule: metaid_0000085
parameter: 028059
compartment: 023948
reaction: 027981
reaction: 027994
species: metaid_0000082
reaction: 028000
notes: This model 2 described in the supplement of the article below. It is parameterized for the WT at 24°C. To reproduce figure 6 the results have to be rescaled to circadian time by multiplying time by 24/ tau , with tau being the period of the free-running oscillator. For the wild-type parameter set tau is equal to 22.7149. Article: Isoform switching facilitates period control in the Neurospora crassa circadian clock. Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA. Mol Syst Biol. 2008;4:164. Epub 2008 Feb 12. PMID: 18277380 , doi: 10.1038/msb.2008.5 Abstract: A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A.…
species: 027963
species: 027953
parameter: 028086
parameter: 028099
reaction: 027979
reaction: 028024
reaction: 028006
species: 027961
parameter: 028089
parameter: 028102
parameter: 028036
species: 027969
is described by: http://identifiers.org/pubmed/18277380
substance units: metaid_0000088
parameter: 028075
parameter: 028041
reaction: 028014
is version of: GO:0042752
parameter: 028057
species: metaid_0000081
parameter: 028039
reaction: 027992
parameter: 028068
species: metaid_0000080
area units: metaid_0000005
species: 027951
parameter: 028096
parameter: 028070
reaction: 027998
parameter: 028052
reaction: 028022
length unit: length
reaction: 028004
units def: metaid_0000087
parameter: 028112
parameter: 028032
parameter: 028034
species: 027967

027951
constant: false
initial amount: NaN
is version of: P19970
type: Species
is: SBO:0000252
in compartment: 027948
boundary condition: false
name: s-Frq_1
initial concentration: 0.43076
has only substance units: false

724036
stoichiometry: 1.0
species: 027965
type: SpeciesReference

028075
constant: true
value: 0.09292
name: f1
type: Parameter

027979
kinetic law: 723807
reactant: 723795
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: MFdeg
type: Reaction

724243
stoichiometry: 1.0
species: 027971
type: SpeciesReference

027961
initial concentration: 5.70265
boundary condition: false
name: WC-1_2
initial amount: NaN
has only substance units: false
is: SBO:0000252
in compartment: 027948
type: Species
is version of: Q01371
constant: false

027971
constant: false
boundary condition: false
initial concentration: 26.4393
in compartment: 023948
name: WC-1
has only substance units: false
initial amount: NaN
is version of: Q01371
type: Species
is: SBO:0000252

028061
constant: true
value: 93.03664
name: b10
type: Parameter

027969
has only substance units: false
boundary condition: false
in compartment: 023948
initial amount: NaN
constant: false
type: Species
name: l-Frq
initial concentration: 0.07719
is version of: P19970
is: SBO:0000252

metaid_0000080
initial amount: NaN
name: tot l-Frq
constant: false
in compartment: 023948
initial concentration: NaN
is version of: P19970
type: Species
is: SBO:0000252
has only substance units: false
boundary condition: false

028041
constant: true
value: 3.02856
name: a7
type: Parameter

028055
constant: true
value: 2.96739
name: b7
type: Parameter

027996
kinetic law: 724048
reactant: 724036
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: MWdeg
type: Reaction

metaid_0000079
type: Species
is version of: P19970
is: SBO:0000252
in compartment: 023948
name: tot s-Frq
initial concentration: NaN
constant: false
has only substance units: false
initial amount: NaN
boundary condition: false

028064
constant: true
value: 1.43549
name: d1
type: Parameter

723723
stoichiometry: 1.0
species: 027963
type: SpeciesReference

724158
stoichiometry: 1.0
species: 027961
type: SpeciesReference

724219
stoichiometry: 1.0
species: 027971
type: SpeciesReference

028039
constant: true
value: 0.20695
name: a6
type: Parameter

028002
kinetic law: 724170
product: 724158
reactant: 724146
is version of: GO:0016485
is: SBO:0000181
fast: false
reversible: false
name: E2Wtrl
type: Reaction

724000
stoichiometry: 1.0
species: 027965
type: SpeciesReference

028361
constant: true
value: 0.0
name: b6
type: Parameter

028099
constant: true
value: 0.18191
name: d2p
type: Parameter

028022
kinetic law: 724471
product: 724459
reactant: 724447
is version of: GO:0006606
is: SBO:0000185
fast: false
reversible: false
name: PFptrl
type: Reaction

028059
constant: true
value: 81.10381
name: b9
type: Parameter

723795
stoichiometry: 1.0
species: 027963
type: SpeciesReference

028012
kinetic law: 724315
reactant: 724303
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: PWLdeg
type: Reaction

028102
constant: true
value: 0.09588
name: f1p
type: Parameter

723951
stoichiometry: 1.0
species: 027967
type: SpeciesReference

723855
stoichiometry: 1.0
species: 027951
type: SpeciesReference

724060
stoichiometry: 1.0
species: 027955
type: SpeciesReference

027953
initial amount: NaN
boundary condition: false
is version of: P19970
constant: false
is: SBO:0000252
type: Species
in compartment: 027948
has only substance units: false
name: l-Frq_1
initial concentration: 0.45583

028073
constant: true
value: 0.41085
name: d5
type: Parameter

027948
is: GO:0005829
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytosol
type: Compartment

027967
has only substance units: false
in compartment: 023948
is: SBO:0000252
boundary condition: false
initial amount: NaN
type: Species
constant: false
initial concentration: 0.06565
is version of: P19970
name: s-Frq

metaid_0000082
name: tot WC-1
is: SBO:0000252
is version of: Q01371
type: Species
boundary condition: false
has only substance units: false
in compartment: 023948
constant: false
initial concentration: NaN
initial amount: NaN

724182
stoichiometry: 1.0
species: 027961
type: SpeciesReference

028043
constant: true
value: 0.00209
name: b1
type: Parameter

724447
stoichiometry: 1.0
species: 027959
type: SpeciesReference

028086
constant: true
value: 35.40005
name: r2
type: Parameter

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

027994
kinetic law: 724024
modifier: 724012
product: 724000
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: MWtrn
type: Reaction

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

given: Ozgur
family: Akman

ORG:
  orgname: Centre for Systems Biology at Edinburgh, The University of Edinburgh, Edinburgh, UK

W3 CDTF: Thu Aug 20 18:35:46 BST 2009

W3 CDTF: Wed Dec 03 12:40:28 GMT 2008